
% Gather parameters for a specific species.
% Possible options are:
% 'Arbacia', 'Lpictus', 'Lvariegatus', 'Human-low', 'Human-high',
% 'Spurpuratus', 'Bull', 'Ciona', 'Zerbrafish', and 'Abalone'

function params = fetch_parameters(species)

params = struct([]);

params(1).tail_pts_to_remove = 2;
params(1).tail_pts_to_remove = 0;
params(1).variable_length = 0;
params(1).eccentric = 0;
params(1).time_res = 750; %fps
params(1).space_res = 17/40; %um/pixel
params(1).pixels_btwn_pts = 3; %

if strcmp(species, 'Abalone')
    params(1).folder = ['130816_abalone_HSOnly' filesep];
    params(1).file_nums = [3, 5, 6, 10, 15, 19];
    params(1).time_res = 419.5; %fps 15x, 123um or 135um deep
    params(1).space_res = 0.4333; % um/pixel
    params(1).variable_length = 1;
    
elseif strcmp(species, 'Arbacia')
    params(1).folder = ['110822_arbacia_HSOnly' filesep];
    params(1).file_nums = [36,37,39]; %38, also 7 of 110923 also seems fine JE 10/31/19
    %New as of 10/31/19 - NO: different conditions
    %params(1).folder = '191031_Arbacia_all\';
    %params(1).file_nums = [3,7,9,10,15:17,10,25:27,36:43];
    
elseif strcmp(species, 'Bull')
    params(1).folder = ['130125_Bull_Friedrich_HSOnly' filesep];
    params(1).file_nums = 1;
    params(1).time_res = 250; % fps -
    params(1).space_res = 20/151; % um/pixel
    params(1).pixels_btwn_pts = 17;
    
elseif strcmp(species, 'Ciona')
    params(1).folder = ['130220_CionaIntestinalis_HSOnly' filesep];
    params(1).file_nums = [1:3 5:7];
%     params(1).tail_pts_to_remove = 3;

elseif strcmp(species, 'Human-low')
    params(1).folder = '130513_HumanSperm_HSOnly\';
    params(1).file_nums = 19:21;
    params(1).time_res = 413.59; %fps
    params(1).space_res = 0.4333; % um/pixel
%     params(1).space_res = 6.5/10; % um/pixel
    params(1).eccentric = 1;
    params(1).variable_length = 1;

elseif strcmp(species, 'Human-high')
    params(1).folder = ['130513_HumanSperm_HSOnly' filesep];
    params(1).file_nums = 15:16;
    params(1).time_res = 413.59; %fps
    params(1).space_res = 0.4333; % um/pixel
    params(1).eccentric = 1;
%     params(1).space_res = 17/15; % um/pixel
    params(1).variable_length = 1;
%     params(1).tail_pts_to_remove = 3;
    
elseif strcmp(species, 'Lpictus')
    params(1).folder = ['120920_lpictus_lvariegatus_HSOnly' filesep];
    params(1).file_nums = 1:6;
%     params(1).tail_pts_to_remove = 4;
    %New as of 10/31/19
    params(1).folder = ['200512_LPictus_all' filesep];
    params(1).file_nums = [1:6,101:106];

elseif strcmp(species, 'Lvariegatus')
    params(1).folder = ['120920_lpictus_lvariegatus_HSOnly' filesep];
    params(1).file_nums = 7:9;
    %New as of 10/31/19
    params(1).folder = ['200512_LVariegatus_all' filesep];
    params(1).file_nums = [7:12,107:112];

elseif strcmp(species, 'Spurpuratus')
    params(1).folder = '130123_Spurpuratus_HSOnly\';
    params(1).file_nums = [1 4 7];
    %New as of 10/31/19
    params(1).folder = '130123_Spurpuratus_HSOnly\';
    params(1).file_nums = [1:9];
    
elseif strcmp(species, 'Zebrafish')
    params(1).folder = ['130403_ZebrafishSperm_HSOnly' filesep];
    params(1).file_nums = 6;
    params(1).file_nums = [6,7,9];
    %New as of 10/31/19 - but are these different conditions?
    params(1).folder = ['191031_Zebrafish_all' filesep];
    params(1).file_nums = [6,7,9,101,102,105,106];
    
    params(1).space_res = 17/60;
    params(1).variable_length = 1;
    
else
    fprintf('No parameters for: %s', species) 
end